Multiple sequence alignment - TraesCS3D01G051400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G051400 chr3D 100.000 2965 0 0 961 3925 20347819 20344855 0.000000e+00 5476.0
1 TraesCS3D01G051400 chr3D 100.000 682 0 0 1 682 20348779 20348098 0.000000e+00 1260.0
2 TraesCS3D01G051400 chr3B 93.931 2175 110 13 978 3144 32749435 32747275 0.000000e+00 3265.0
3 TraesCS3D01G051400 chr3B 81.130 885 149 12 1039 1920 23032898 23032029 0.000000e+00 693.0
4 TraesCS3D01G051400 chr3B 91.684 469 34 3 215 682 32750718 32750254 0.000000e+00 645.0
5 TraesCS3D01G051400 chr3B 87.892 446 40 10 3152 3588 32747040 32746600 2.700000e-141 512.0
6 TraesCS3D01G051400 chr3B 95.146 206 8 1 17 222 32752594 32752391 1.360000e-84 324.0
7 TraesCS3D01G051400 chr3A 91.697 1626 87 23 2035 3622 28126652 28125037 0.000000e+00 2211.0
8 TraesCS3D01G051400 chr3A 94.654 1085 50 7 961 2040 28127918 28126837 0.000000e+00 1676.0
9 TraesCS3D01G051400 chr3A 81.081 925 157 12 1000 1920 20491933 20492843 0.000000e+00 723.0
10 TraesCS3D01G051400 chr3A 91.667 336 26 2 209 543 28129542 28129208 7.680000e-127 464.0
11 TraesCS3D01G051400 chr3A 90.909 308 28 0 268 575 28131214 28130907 7.850000e-112 414.0
12 TraesCS3D01G051400 chr3A 95.567 203 9 0 21 223 28131575 28131373 3.780000e-85 326.0
13 TraesCS3D01G051400 chr3A 94.340 159 9 0 64 222 28129729 28129571 1.090000e-60 244.0
14 TraesCS3D01G051400 chr3A 92.617 149 5 4 535 682 28129034 28128891 3.970000e-50 209.0
15 TraesCS3D01G051400 chr3A 84.615 169 13 6 3704 3859 498233746 498233578 5.250000e-34 156.0
16 TraesCS3D01G051400 chr3A 92.593 108 5 1 575 682 28130184 28130080 6.790000e-33 152.0
17 TraesCS3D01G051400 chr3A 92.754 69 4 1 210 277 28131343 28131275 8.980000e-17 99.0
18 TraesCS3D01G051400 chr1D 90.743 929 84 2 993 1920 446647556 446646629 0.000000e+00 1238.0
19 TraesCS3D01G051400 chr1D 86.364 638 83 3 2291 2925 446644341 446643705 0.000000e+00 693.0
20 TraesCS3D01G051400 chr1A 89.892 930 90 4 993 1920 542371358 542370431 0.000000e+00 1194.0
21 TraesCS3D01G051400 chr1B 89.355 930 95 4 993 1920 611675890 611676817 0.000000e+00 1166.0
22 TraesCS3D01G051400 chr1B 85.692 636 89 2 2291 2925 611680706 611681340 0.000000e+00 669.0
23 TraesCS3D01G051400 chr1B 100.000 33 0 0 3638 3670 533196809 533196841 1.180000e-05 62.1
24 TraesCS3D01G051400 chr7A 82.217 866 145 8 995 1857 546060947 546060088 0.000000e+00 737.0
25 TraesCS3D01G051400 chr7A 97.059 34 1 0 2053 2086 514822342 514822309 1.520000e-04 58.4
26 TraesCS3D01G051400 chr7A 92.105 38 3 0 2054 2091 626415002 626414965 2.000000e-03 54.7
27 TraesCS3D01G051400 chr2D 77.973 740 146 12 1107 1834 589318430 589317696 7.740000e-122 448.0
28 TraesCS3D01G051400 chr2B 86.580 231 16 8 3704 3922 133551717 133551944 1.410000e-59 241.0
29 TraesCS3D01G051400 chr6A 86.404 228 20 6 3707 3923 203767697 203767470 5.070000e-59 239.0
30 TraesCS3D01G051400 chr6A 85.027 187 11 7 3704 3877 18837282 18837464 1.450000e-39 174.0
31 TraesCS3D01G051400 chr6A 90.698 43 4 0 2051 2093 38756988 38757030 1.520000e-04 58.4
32 TraesCS3D01G051400 chr6D 84.914 232 21 10 3704 3923 115813989 115814218 5.100000e-54 222.0
33 TraesCS3D01G051400 chr7D 84.112 214 17 7 3704 3905 530895220 530895428 1.440000e-44 191.0
34 TraesCS3D01G051400 chr7D 83.158 190 21 6 3727 3911 602719707 602719890 3.140000e-36 163.0
35 TraesCS3D01G051400 chr6B 78.947 228 24 5 3707 3923 638916316 638916530 2.460000e-27 134.0
36 TraesCS3D01G051400 chr5A 88.421 95 11 0 3829 3923 494411267 494411173 8.910000e-22 115.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G051400 chr3D 20344855 20348779 3924 True 3368.000000 5476 100.000000 1 3925 2 chr3D.!!$R1 3924
1 TraesCS3D01G051400 chr3B 32746600 32752594 5994 True 1186.500000 3265 92.163250 17 3588 4 chr3B.!!$R2 3571
2 TraesCS3D01G051400 chr3B 23032029 23032898 869 True 693.000000 693 81.130000 1039 1920 1 chr3B.!!$R1 881
3 TraesCS3D01G051400 chr3A 20491933 20492843 910 False 723.000000 723 81.081000 1000 1920 1 chr3A.!!$F1 920
4 TraesCS3D01G051400 chr3A 28125037 28131575 6538 True 643.888889 2211 92.977556 21 3622 9 chr3A.!!$R2 3601
5 TraesCS3D01G051400 chr1D 446643705 446647556 3851 True 965.500000 1238 88.553500 993 2925 2 chr1D.!!$R1 1932
6 TraesCS3D01G051400 chr1A 542370431 542371358 927 True 1194.000000 1194 89.892000 993 1920 1 chr1A.!!$R1 927
7 TraesCS3D01G051400 chr1B 611675890 611681340 5450 False 917.500000 1166 87.523500 993 2925 2 chr1B.!!$F2 1932
8 TraesCS3D01G051400 chr7A 546060088 546060947 859 True 737.000000 737 82.217000 995 1857 1 chr7A.!!$R2 862
9 TraesCS3D01G051400 chr2D 589317696 589318430 734 True 448.000000 448 77.973000 1107 1834 1 chr2D.!!$R1 727

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
388 2141 0.036732 TTCTCTGCTGGCACCGAATT 59.963 50.0 0.00 0.00 0.0 2.17 F
1638 6079 0.967887 TCCAGGAGTTCTCGAGGCTG 60.968 60.0 13.56 1.27 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 6338 1.934589 TTGACATTATCCCGCGTGAG 58.065 50.0 4.92 0.00 0.00 3.51 R
2946 11581 0.321564 GTCTATGTGGGCACTGCACA 60.322 55.0 0.41 0.41 40.85 4.57 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 126 2.226437 GTGCCGTTTGATCACATCACTT 59.774 45.455 0.00 0.00 39.39 3.16
183 184 1.736126 CATGTGCCTAGCTTGACACAG 59.264 52.381 20.13 10.32 45.39 3.66
270 1953 7.840342 ATAAAACAAACACACAATTCTGCAA 57.160 28.000 0.00 0.00 0.00 4.08
277 1960 3.701040 ACACACAATTCTGCAAAACTCCT 59.299 39.130 0.00 0.00 0.00 3.69
292 2045 6.146021 GCAAAACTCCTTATGTCCACAATTTG 59.854 38.462 0.00 0.00 0.00 2.32
299 2052 5.480642 TTATGTCCACAATTTGGTTGCAT 57.519 34.783 0.78 3.37 46.97 3.96
307 2060 7.548780 GTCCACAATTTGGTTGCATATACAATT 59.451 33.333 0.78 0.00 46.97 2.32
311 2064 9.801873 ACAATTTGGTTGCATATACAATTCTAC 57.198 29.630 0.78 0.00 41.69 2.59
313 2066 8.766994 ATTTGGTTGCATATACAATTCTACCT 57.233 30.769 0.00 0.00 0.00 3.08
337 2090 6.641062 TGTGTTTTAAAAATTCCGCGAATTG 58.359 32.000 8.23 0.00 40.77 2.32
379 2132 1.372087 GGGCGACAATTCTCTGCTGG 61.372 60.000 0.00 0.00 0.00 4.85
388 2141 0.036732 TTCTCTGCTGGCACCGAATT 59.963 50.000 0.00 0.00 0.00 2.17
398 2151 3.531538 TGGCACCGAATTCTAGAATGAC 58.468 45.455 18.61 10.10 0.00 3.06
626 3103 6.500684 TTGAAAGGTGCTTAGCTAGAAATG 57.499 37.500 5.60 0.00 0.00 2.32
981 5399 1.153568 GCTAGGCAGTGATCGTGCA 60.154 57.895 18.62 1.98 43.12 4.57
1005 5423 2.004017 TCGTTCGTATTGTCAATGGCC 58.996 47.619 8.39 0.00 0.00 5.36
1017 5435 1.487976 TCAATGGCCACCTTTGCAAAA 59.512 42.857 8.16 0.00 38.19 2.44
1132 5558 4.995058 TTCCTCCGGGGCCCAAGT 62.995 66.667 26.86 0.00 34.39 3.16
1436 5862 1.078214 CCAAGATCTTCAGCCGCCA 60.078 57.895 4.57 0.00 0.00 5.69
1638 6079 0.967887 TCCAGGAGTTCTCGAGGCTG 60.968 60.000 13.56 1.27 0.00 4.85
1882 6338 3.894947 GAGAGGACGCTCTCCGCC 61.895 72.222 8.44 0.00 45.10 6.13
1975 7104 4.257267 TCACACATCTCACGAACTTCAT 57.743 40.909 0.00 0.00 0.00 2.57
1978 7107 5.177511 TCACACATCTCACGAACTTCATTTC 59.822 40.000 0.00 0.00 0.00 2.17
2033 10607 2.650322 TCTTTTTGTTGCGAGGGAGTT 58.350 42.857 0.00 0.00 0.00 3.01
2040 10614 2.753452 TGTTGCGAGGGAGTTCTACTAG 59.247 50.000 0.00 0.00 0.00 2.57
2086 10699 4.320870 GACAAGTATTTTGGAACCGAGGA 58.679 43.478 0.00 0.00 0.00 3.71
2243 10865 3.632145 TGACTGCCTGAAAGAAAAGGAAC 59.368 43.478 0.00 0.00 35.40 3.62
2246 10868 4.038402 ACTGCCTGAAAGAAAAGGAACATG 59.962 41.667 0.00 0.00 35.40 3.21
2315 10948 2.953284 TGTTATTTGGTGGACCGGAA 57.047 45.000 9.46 0.00 39.43 4.30
2318 10951 2.203470 TATTTGGTGGACCGGAAACC 57.797 50.000 9.46 13.35 39.43 3.27
2360 10993 1.867615 GATGGCAGAGATGATGCGC 59.132 57.895 0.00 0.00 44.80 6.09
2946 11581 9.693739 TGTAATGTGATAATTATTGGACAAGGT 57.306 29.630 0.00 0.00 0.00 3.50
2961 11596 2.598394 GGTGTGCAGTGCCCACAT 60.598 61.111 28.18 0.00 44.16 3.21
2990 11625 8.026607 ACGTAACATTATATTGCCAATAATGCC 58.973 33.333 16.61 8.68 45.20 4.40
2991 11626 8.026026 CGTAACATTATATTGCCAATAATGCCA 58.974 33.333 16.61 7.32 45.20 4.92
3073 11708 5.512232 CCCTAAATTTAGCAAAGTTTGGCCA 60.512 40.000 18.18 0.00 39.08 5.36
3074 11709 5.994668 CCTAAATTTAGCAAAGTTTGGCCAA 59.005 36.000 16.05 16.05 35.37 4.52
3083 11718 4.555262 CAAAGTTTGGCCAATTATCACGT 58.445 39.130 21.26 9.51 0.00 4.49
3084 11719 3.848272 AGTTTGGCCAATTATCACGTG 57.152 42.857 21.26 9.94 0.00 4.49
3085 11720 3.153919 AGTTTGGCCAATTATCACGTGT 58.846 40.909 21.26 5.66 0.00 4.49
3086 11721 3.057596 AGTTTGGCCAATTATCACGTGTG 60.058 43.478 21.26 5.75 0.00 3.82
3087 11722 2.192664 TGGCCAATTATCACGTGTGT 57.807 45.000 16.51 8.40 0.00 3.72
3130 11769 2.632377 ACACATCCGACCATTGTCATC 58.368 47.619 0.00 0.00 41.85 2.92
3146 11785 1.480545 TCATCGTGAACCATCATCGGT 59.519 47.619 0.00 0.00 42.71 4.69
3198 12066 7.838696 AGAGAGAGAGAGAGAATTATTTGGTCA 59.161 37.037 0.00 0.00 0.00 4.02
3215 12086 6.839124 TTGGTCATACAAATGCTGATCTTT 57.161 33.333 0.00 0.00 32.76 2.52
3329 12203 6.094048 GCCTTTCTCATTTAGCATGTAAGTGA 59.906 38.462 0.00 4.24 0.00 3.41
3367 12245 1.673168 GAGCTGGCTAAAGATGGGTG 58.327 55.000 0.00 0.00 0.00 4.61
3470 12348 3.058016 ACAAAATTGACATGTGAGCGAGG 60.058 43.478 1.15 0.00 0.00 4.63
3481 12359 1.409427 GTGAGCGAGGTATAAGCCTGT 59.591 52.381 0.00 0.00 39.34 4.00
3504 12382 6.177610 GTTGTTGTATTTACTCTGATCCCCA 58.822 40.000 0.00 0.00 0.00 4.96
3509 12387 5.365605 TGTATTTACTCTGATCCCCACGATT 59.634 40.000 0.00 0.00 0.00 3.34
3518 12396 0.906775 TCCCCACGATTACTTGGACC 59.093 55.000 0.00 0.00 37.59 4.46
3544 12423 4.953868 CGACCGCGACCACCACAA 62.954 66.667 8.23 0.00 40.82 3.33
3545 12424 3.041940 GACCGCGACCACCACAAG 61.042 66.667 8.23 0.00 0.00 3.16
3556 12435 0.896940 CACCACAAGCTGCCCAAGAT 60.897 55.000 0.00 0.00 0.00 2.40
3614 12497 1.654137 GTGTGTTTGCGCGTCAAGG 60.654 57.895 8.43 0.00 35.84 3.61
3615 12498 2.109739 TGTGTTTGCGCGTCAAGGT 61.110 52.632 8.43 0.00 35.84 3.50
3616 12499 1.654137 GTGTTTGCGCGTCAAGGTG 60.654 57.895 8.43 0.00 35.84 4.00
3617 12500 1.815840 TGTTTGCGCGTCAAGGTGA 60.816 52.632 8.43 0.00 35.84 4.02
3619 12502 0.040425 GTTTGCGCGTCAAGGTGAAT 60.040 50.000 8.43 0.00 35.84 2.57
3620 12503 1.195900 GTTTGCGCGTCAAGGTGAATA 59.804 47.619 8.43 0.00 35.84 1.75
3621 12504 1.075542 TTGCGCGTCAAGGTGAATAG 58.924 50.000 8.43 0.00 0.00 1.73
3622 12505 0.037697 TGCGCGTCAAGGTGAATAGT 60.038 50.000 8.43 0.00 0.00 2.12
3623 12506 0.370273 GCGCGTCAAGGTGAATAGTG 59.630 55.000 8.43 0.00 0.00 2.74
3624 12507 0.370273 CGCGTCAAGGTGAATAGTGC 59.630 55.000 0.00 0.00 0.00 4.40
3625 12508 1.726853 GCGTCAAGGTGAATAGTGCT 58.273 50.000 0.00 0.00 0.00 4.40
3626 12509 1.394917 GCGTCAAGGTGAATAGTGCTG 59.605 52.381 0.00 0.00 0.00 4.41
3627 12510 2.930887 GCGTCAAGGTGAATAGTGCTGA 60.931 50.000 0.00 0.00 0.00 4.26
3628 12511 2.926200 CGTCAAGGTGAATAGTGCTGAG 59.074 50.000 0.00 0.00 0.00 3.35
3629 12512 3.367395 CGTCAAGGTGAATAGTGCTGAGA 60.367 47.826 0.00 0.00 0.00 3.27
3630 12513 4.679106 CGTCAAGGTGAATAGTGCTGAGAT 60.679 45.833 0.00 0.00 0.00 2.75
3631 12514 4.569966 GTCAAGGTGAATAGTGCTGAGATG 59.430 45.833 0.00 0.00 0.00 2.90
3632 12515 4.223700 TCAAGGTGAATAGTGCTGAGATGT 59.776 41.667 0.00 0.00 0.00 3.06
3633 12516 5.422012 TCAAGGTGAATAGTGCTGAGATGTA 59.578 40.000 0.00 0.00 0.00 2.29
3634 12517 5.269505 AGGTGAATAGTGCTGAGATGTAC 57.730 43.478 0.00 0.00 0.00 2.90
3635 12518 4.959210 AGGTGAATAGTGCTGAGATGTACT 59.041 41.667 0.00 0.00 36.82 2.73
3636 12519 6.129874 AGGTGAATAGTGCTGAGATGTACTA 58.870 40.000 0.00 0.00 38.94 1.82
3637 12520 6.264292 AGGTGAATAGTGCTGAGATGTACTAG 59.736 42.308 0.00 0.00 38.24 2.57
3638 12521 6.039941 GGTGAATAGTGCTGAGATGTACTAGT 59.960 42.308 0.00 0.00 38.24 2.57
3639 12522 7.228906 GGTGAATAGTGCTGAGATGTACTAGTA 59.771 40.741 0.00 0.00 38.24 1.82
3640 12523 8.788806 GTGAATAGTGCTGAGATGTACTAGTAT 58.211 37.037 5.75 0.00 38.24 2.12
3645 12528 8.698973 AGTGCTGAGATGTACTAGTATATTGT 57.301 34.615 12.80 4.74 31.35 2.71
3646 12529 8.572185 AGTGCTGAGATGTACTAGTATATTGTG 58.428 37.037 12.80 6.20 31.35 3.33
3647 12530 7.327275 GTGCTGAGATGTACTAGTATATTGTGC 59.673 40.741 12.80 13.88 0.00 4.57
3648 12531 7.014230 TGCTGAGATGTACTAGTATATTGTGCA 59.986 37.037 12.80 15.70 34.26 4.57
3649 12532 8.031864 GCTGAGATGTACTAGTATATTGTGCAT 58.968 37.037 12.80 6.61 41.21 3.96
3650 12533 9.351570 CTGAGATGTACTAGTATATTGTGCATG 57.648 37.037 12.80 0.00 39.33 4.06
3651 12534 8.860088 TGAGATGTACTAGTATATTGTGCATGT 58.140 33.333 12.80 5.42 39.33 3.21
3652 12535 9.347934 GAGATGTACTAGTATATTGTGCATGTC 57.652 37.037 12.80 10.09 40.39 3.06
3653 12536 9.083422 AGATGTACTAGTATATTGTGCATGTCT 57.917 33.333 12.80 1.63 39.33 3.41
3662 12545 9.618890 AGTATATTGTGCATGTCTATTTCTTGT 57.381 29.630 0.00 0.00 0.00 3.16
3665 12548 7.686438 ATTGTGCATGTCTATTTCTTGTACA 57.314 32.000 0.00 0.00 35.31 2.90
3666 12549 7.503521 TTGTGCATGTCTATTTCTTGTACAA 57.496 32.000 8.28 8.28 40.26 2.41
3667 12550 6.898041 TGTGCATGTCTATTTCTTGTACAAC 58.102 36.000 3.59 0.00 34.67 3.32
3668 12551 6.484977 TGTGCATGTCTATTTCTTGTACAACA 59.515 34.615 3.59 0.00 34.67 3.33
3669 12552 7.012799 TGTGCATGTCTATTTCTTGTACAACAA 59.987 33.333 3.59 0.00 34.67 2.83
3670 12553 8.023128 GTGCATGTCTATTTCTTGTACAACAAT 58.977 33.333 3.59 8.60 37.48 2.71
3671 12554 8.575589 TGCATGTCTATTTCTTGTACAACAATT 58.424 29.630 3.59 0.38 37.48 2.32
3672 12555 9.065871 GCATGTCTATTTCTTGTACAACAATTC 57.934 33.333 3.59 2.56 37.48 2.17
3675 12558 8.289618 TGTCTATTTCTTGTACAACAATTCTGC 58.710 33.333 3.59 0.00 37.48 4.26
3676 12559 8.507249 GTCTATTTCTTGTACAACAATTCTGCT 58.493 33.333 3.59 0.00 37.48 4.24
3677 12560 9.719355 TCTATTTCTTGTACAACAATTCTGCTA 57.281 29.630 3.59 0.00 37.48 3.49
3681 12564 9.862371 TTTCTTGTACAACAATTCTGCTAAAAA 57.138 25.926 3.59 0.00 37.48 1.94
3682 12565 8.850454 TCTTGTACAACAATTCTGCTAAAAAC 57.150 30.769 3.59 0.00 37.48 2.43
3683 12566 8.682710 TCTTGTACAACAATTCTGCTAAAAACT 58.317 29.630 3.59 0.00 37.48 2.66
3684 12567 9.944663 CTTGTACAACAATTCTGCTAAAAACTA 57.055 29.630 3.59 0.00 37.48 2.24
3688 12571 8.728088 ACAACAATTCTGCTAAAAACTAATCG 57.272 30.769 0.00 0.00 0.00 3.34
3689 12572 7.326063 ACAACAATTCTGCTAAAAACTAATCGC 59.674 33.333 0.00 0.00 0.00 4.58
3690 12573 7.145932 ACAATTCTGCTAAAAACTAATCGCT 57.854 32.000 0.00 0.00 0.00 4.93
3691 12574 8.263940 ACAATTCTGCTAAAAACTAATCGCTA 57.736 30.769 0.00 0.00 0.00 4.26
3692 12575 8.391106 ACAATTCTGCTAAAAACTAATCGCTAG 58.609 33.333 0.00 0.00 0.00 3.42
3693 12576 6.903883 TTCTGCTAAAAACTAATCGCTAGG 57.096 37.500 0.00 0.00 31.14 3.02
3694 12577 5.357257 TCTGCTAAAAACTAATCGCTAGGG 58.643 41.667 0.00 0.00 31.14 3.53
3695 12578 5.128171 TCTGCTAAAAACTAATCGCTAGGGA 59.872 40.000 12.40 12.40 31.14 4.20
3696 12579 5.925509 TGCTAAAAACTAATCGCTAGGGAT 58.074 37.500 16.12 16.12 31.14 3.85
3697 12580 7.014905 TCTGCTAAAAACTAATCGCTAGGGATA 59.985 37.037 21.39 9.88 31.14 2.59
3698 12581 6.927381 TGCTAAAAACTAATCGCTAGGGATAC 59.073 38.462 21.39 3.89 31.14 2.24
3699 12582 6.089150 GCTAAAAACTAATCGCTAGGGATACG 59.911 42.308 21.39 16.77 37.60 3.06
3700 12583 3.572604 AACTAATCGCTAGGGATACGC 57.427 47.619 21.39 0.00 37.60 4.42
3702 12585 0.806868 TAATCGCTAGGGATACGCGG 59.193 55.000 21.39 0.00 46.23 6.46
3703 12586 2.488087 AATCGCTAGGGATACGCGGC 62.488 60.000 21.39 0.00 46.23 6.53
3704 12587 4.719369 CGCTAGGGATACGCGGCC 62.719 72.222 12.47 8.88 42.88 6.13
3705 12588 3.303928 GCTAGGGATACGCGGCCT 61.304 66.667 12.47 0.00 37.60 5.19
3706 12589 2.963371 CTAGGGATACGCGGCCTC 59.037 66.667 12.47 3.41 37.60 4.70
3707 12590 2.599578 TAGGGATACGCGGCCTCC 60.600 66.667 12.47 13.15 37.60 4.30
3725 12608 4.821589 CCGCAGCGGGAGAGAACC 62.822 72.222 27.32 0.00 44.15 3.62
3726 12609 4.821589 CGCAGCGGGAGAGAACCC 62.822 72.222 7.00 0.00 45.92 4.11
3727 12610 4.475135 GCAGCGGGAGAGAACCCC 62.475 72.222 0.00 0.00 46.62 4.95
3728 12611 3.003173 CAGCGGGAGAGAACCCCA 61.003 66.667 0.00 0.00 46.62 4.96
3729 12612 3.003763 AGCGGGAGAGAACCCCAC 61.004 66.667 0.00 0.00 46.62 4.61
3730 12613 4.097361 GCGGGAGAGAACCCCACC 62.097 72.222 0.00 0.00 46.62 4.61
3731 12614 3.771160 CGGGAGAGAACCCCACCG 61.771 72.222 0.00 0.00 46.62 4.94
3732 12615 4.097361 GGGAGAGAACCCCACCGC 62.097 72.222 0.00 0.00 43.81 5.68
3733 12616 4.097361 GGAGAGAACCCCACCGCC 62.097 72.222 0.00 0.00 0.00 6.13
3734 12617 4.452733 GAGAGAACCCCACCGCCG 62.453 72.222 0.00 0.00 0.00 6.46
3752 12635 4.598894 CCGCCGCCTGATCTCCTG 62.599 72.222 0.00 0.00 0.00 3.86
3754 12637 4.925861 GCCGCCTGATCTCCTGCC 62.926 72.222 0.00 0.00 0.00 4.85
3755 12638 3.160047 CCGCCTGATCTCCTGCCT 61.160 66.667 0.00 0.00 0.00 4.75
3756 12639 2.420890 CGCCTGATCTCCTGCCTC 59.579 66.667 0.00 0.00 0.00 4.70
3757 12640 2.828145 GCCTGATCTCCTGCCTCC 59.172 66.667 0.00 0.00 0.00 4.30
3758 12641 3.136750 CCTGATCTCCTGCCTCCG 58.863 66.667 0.00 0.00 0.00 4.63
3759 12642 2.506061 CCTGATCTCCTGCCTCCGG 61.506 68.421 0.00 0.00 0.00 5.14
3770 12653 3.787001 CCTCCGGCCACCTCCTTC 61.787 72.222 2.24 0.00 0.00 3.46
3771 12654 3.003173 CTCCGGCCACCTCCTTCA 61.003 66.667 2.24 0.00 0.00 3.02
3772 12655 3.316573 CTCCGGCCACCTCCTTCAC 62.317 68.421 2.24 0.00 0.00 3.18
3773 12656 3.636231 CCGGCCACCTCCTTCACA 61.636 66.667 2.24 0.00 0.00 3.58
3774 12657 2.429930 CGGCCACCTCCTTCACAA 59.570 61.111 2.24 0.00 0.00 3.33
3775 12658 1.966451 CGGCCACCTCCTTCACAAC 60.966 63.158 2.24 0.00 0.00 3.32
3776 12659 1.150536 GGCCACCTCCTTCACAACA 59.849 57.895 0.00 0.00 0.00 3.33
3777 12660 0.890996 GGCCACCTCCTTCACAACAG 60.891 60.000 0.00 0.00 0.00 3.16
3778 12661 0.108585 GCCACCTCCTTCACAACAGA 59.891 55.000 0.00 0.00 0.00 3.41
3779 12662 1.879796 GCCACCTCCTTCACAACAGAG 60.880 57.143 0.00 0.00 0.00 3.35
3780 12663 1.694150 CCACCTCCTTCACAACAGAGA 59.306 52.381 0.00 0.00 0.00 3.10
3781 12664 2.548920 CCACCTCCTTCACAACAGAGAC 60.549 54.545 0.00 0.00 0.00 3.36
3782 12665 2.366916 CACCTCCTTCACAACAGAGACT 59.633 50.000 0.00 0.00 0.00 3.24
3783 12666 3.574396 CACCTCCTTCACAACAGAGACTA 59.426 47.826 0.00 0.00 0.00 2.59
3784 12667 3.829601 ACCTCCTTCACAACAGAGACTAG 59.170 47.826 0.00 0.00 0.00 2.57
3785 12668 4.082845 CCTCCTTCACAACAGAGACTAGA 58.917 47.826 0.00 0.00 0.00 2.43
3786 12669 4.709397 CCTCCTTCACAACAGAGACTAGAT 59.291 45.833 0.00 0.00 0.00 1.98
3787 12670 5.163561 CCTCCTTCACAACAGAGACTAGATC 60.164 48.000 0.00 0.00 0.00 2.75
3788 12671 5.575157 TCCTTCACAACAGAGACTAGATCT 58.425 41.667 0.00 0.00 41.91 2.75
3790 12673 5.417266 CCTTCACAACAGAGACTAGATCTGA 59.583 44.000 26.05 9.37 45.80 3.27
3791 12674 6.071672 CCTTCACAACAGAGACTAGATCTGAA 60.072 42.308 26.05 14.29 45.80 3.02
3792 12675 6.901081 TCACAACAGAGACTAGATCTGAAA 57.099 37.500 26.05 10.80 45.80 2.69
3793 12676 6.682746 TCACAACAGAGACTAGATCTGAAAC 58.317 40.000 26.05 4.53 45.80 2.78
3794 12677 5.866633 CACAACAGAGACTAGATCTGAAACC 59.133 44.000 26.05 4.25 45.80 3.27
3795 12678 5.046950 ACAACAGAGACTAGATCTGAAACCC 60.047 44.000 26.05 3.71 45.80 4.11
3796 12679 4.941713 ACAGAGACTAGATCTGAAACCCT 58.058 43.478 26.05 8.66 45.80 4.34
3797 12680 4.953579 ACAGAGACTAGATCTGAAACCCTC 59.046 45.833 26.05 3.75 45.80 4.30
3798 12681 5.200483 CAGAGACTAGATCTGAAACCCTCT 58.800 45.833 18.91 5.89 45.80 3.69
3799 12682 5.299279 CAGAGACTAGATCTGAAACCCTCTC 59.701 48.000 18.91 7.05 45.80 3.20
3800 12683 5.193728 AGAGACTAGATCTGAAACCCTCTCT 59.806 44.000 5.18 6.21 38.00 3.10
3801 12684 5.837829 AGACTAGATCTGAAACCCTCTCTT 58.162 41.667 5.18 0.00 35.81 2.85
3802 12685 5.891551 AGACTAGATCTGAAACCCTCTCTTC 59.108 44.000 5.18 0.00 35.81 2.87
3803 12686 5.584913 ACTAGATCTGAAACCCTCTCTTCA 58.415 41.667 5.18 0.00 0.00 3.02
3804 12687 6.201591 ACTAGATCTGAAACCCTCTCTTCAT 58.798 40.000 5.18 0.00 31.40 2.57
3805 12688 5.612725 AGATCTGAAACCCTCTCTTCATC 57.387 43.478 0.00 0.00 31.40 2.92
3806 12689 4.408596 AGATCTGAAACCCTCTCTTCATCC 59.591 45.833 0.00 0.00 31.40 3.51
3807 12690 3.520696 TCTGAAACCCTCTCTTCATCCA 58.479 45.455 0.00 0.00 31.40 3.41
3808 12691 4.107072 TCTGAAACCCTCTCTTCATCCAT 58.893 43.478 0.00 0.00 31.40 3.41
3809 12692 4.163078 TCTGAAACCCTCTCTTCATCCATC 59.837 45.833 0.00 0.00 31.40 3.51
3810 12693 3.200825 TGAAACCCTCTCTTCATCCATCC 59.799 47.826 0.00 0.00 0.00 3.51
3811 12694 1.813102 ACCCTCTCTTCATCCATCCC 58.187 55.000 0.00 0.00 0.00 3.85
3812 12695 0.683973 CCCTCTCTTCATCCATCCCG 59.316 60.000 0.00 0.00 0.00 5.14
3813 12696 0.683973 CCTCTCTTCATCCATCCCGG 59.316 60.000 0.00 0.00 0.00 5.73
3821 12704 2.764128 TCCATCCCGGAGTCCAGC 60.764 66.667 10.49 0.00 39.64 4.85
3822 12705 4.227134 CCATCCCGGAGTCCAGCG 62.227 72.222 10.49 0.00 36.56 5.18
3823 12706 3.147595 CATCCCGGAGTCCAGCGA 61.148 66.667 10.49 0.89 0.00 4.93
3824 12707 2.123251 ATCCCGGAGTCCAGCGAT 60.123 61.111 10.49 3.44 0.00 4.58
3825 12708 2.203771 ATCCCGGAGTCCAGCGATC 61.204 63.158 10.49 0.00 0.00 3.69
3826 12709 3.917760 CCCGGAGTCCAGCGATCC 61.918 72.222 10.49 0.00 0.00 3.36
3827 12710 2.835431 CCGGAGTCCAGCGATCCT 60.835 66.667 10.49 0.00 0.00 3.24
3828 12711 2.415010 CGGAGTCCAGCGATCCTG 59.585 66.667 10.49 4.67 41.41 3.86
3835 12718 3.842923 CAGCGATCCTGGGCGACT 61.843 66.667 12.79 7.29 37.93 4.18
3836 12719 3.532155 AGCGATCCTGGGCGACTC 61.532 66.667 12.79 0.00 0.00 3.36
3837 12720 4.933064 GCGATCCTGGGCGACTCG 62.933 72.222 12.79 0.00 0.00 4.18
3838 12721 3.209812 CGATCCTGGGCGACTCGA 61.210 66.667 1.63 0.00 0.00 4.04
3839 12722 2.725008 GATCCTGGGCGACTCGAG 59.275 66.667 11.84 11.84 0.00 4.04
3840 12723 2.835431 ATCCTGGGCGACTCGAGG 60.835 66.667 18.41 0.17 0.00 4.63
3881 12764 1.393603 GCATAGCCACCTCCTTTTCC 58.606 55.000 0.00 0.00 0.00 3.13
3882 12765 1.064389 GCATAGCCACCTCCTTTTCCT 60.064 52.381 0.00 0.00 0.00 3.36
3883 12766 2.924421 CATAGCCACCTCCTTTTCCTC 58.076 52.381 0.00 0.00 0.00 3.71
3884 12767 1.286248 TAGCCACCTCCTTTTCCTCC 58.714 55.000 0.00 0.00 0.00 4.30
3885 12768 1.000771 GCCACCTCCTTTTCCTCCC 60.001 63.158 0.00 0.00 0.00 4.30
3886 12769 1.501654 GCCACCTCCTTTTCCTCCCT 61.502 60.000 0.00 0.00 0.00 4.20
3887 12770 1.076438 CCACCTCCTTTTCCTCCCTT 58.924 55.000 0.00 0.00 0.00 3.95
3888 12771 1.004862 CCACCTCCTTTTCCTCCCTTC 59.995 57.143 0.00 0.00 0.00 3.46
3889 12772 1.004862 CACCTCCTTTTCCTCCCTTCC 59.995 57.143 0.00 0.00 0.00 3.46
3890 12773 1.132036 ACCTCCTTTTCCTCCCTTCCT 60.132 52.381 0.00 0.00 0.00 3.36
3891 12774 1.562008 CCTCCTTTTCCTCCCTTCCTC 59.438 57.143 0.00 0.00 0.00 3.71
3892 12775 1.208293 CTCCTTTTCCTCCCTTCCTCG 59.792 57.143 0.00 0.00 0.00 4.63
3893 12776 0.393132 CCTTTTCCTCCCTTCCTCGC 60.393 60.000 0.00 0.00 0.00 5.03
3894 12777 0.393132 CTTTTCCTCCCTTCCTCGCC 60.393 60.000 0.00 0.00 0.00 5.54
3895 12778 2.180159 TTTTCCTCCCTTCCTCGCCG 62.180 60.000 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.101741 GTGCTACTTCCTCTGTCCCATAAT 59.898 45.833 0.00 0.00 0.00 1.28
1 2 3.451178 GTGCTACTTCCTCTGTCCCATAA 59.549 47.826 0.00 0.00 0.00 1.90
2 3 3.031736 GTGCTACTTCCTCTGTCCCATA 58.968 50.000 0.00 0.00 0.00 2.74
3 4 1.834263 GTGCTACTTCCTCTGTCCCAT 59.166 52.381 0.00 0.00 0.00 4.00
4 5 1.267121 GTGCTACTTCCTCTGTCCCA 58.733 55.000 0.00 0.00 0.00 4.37
6 7 1.562783 AGGTGCTACTTCCTCTGTCC 58.437 55.000 0.00 0.00 0.00 4.02
7 8 5.346181 AATTAGGTGCTACTTCCTCTGTC 57.654 43.478 0.00 0.00 35.51 3.51
8 9 6.869206 TTAATTAGGTGCTACTTCCTCTGT 57.131 37.500 0.00 0.00 35.51 3.41
9 10 7.331791 ACTTTAATTAGGTGCTACTTCCTCTG 58.668 38.462 0.00 0.00 35.51 3.35
10 11 7.497773 ACTTTAATTAGGTGCTACTTCCTCT 57.502 36.000 0.00 0.00 35.51 3.69
11 12 8.476447 ACTACTTTAATTAGGTGCTACTTCCTC 58.524 37.037 0.00 0.00 35.51 3.71
12 13 8.376803 ACTACTTTAATTAGGTGCTACTTCCT 57.623 34.615 4.19 0.00 37.80 3.36
13 14 8.880750 CAACTACTTTAATTAGGTGCTACTTCC 58.119 37.037 0.00 0.00 27.69 3.46
14 15 9.649167 TCAACTACTTTAATTAGGTGCTACTTC 57.351 33.333 2.96 0.00 34.69 3.01
125 126 4.841813 TGAGTAGTGGAGTTTGGACCATAA 59.158 41.667 0.00 0.00 38.48 1.90
197 198 4.778534 ATTACTCCTCGTCGAAGTTTGA 57.221 40.909 4.98 0.00 0.00 2.69
251 1934 5.237048 AGTTTTGCAGAATTGTGTGTTTGT 58.763 33.333 4.33 0.00 0.00 2.83
292 2045 6.542370 ACACAGGTAGAATTGTATATGCAACC 59.458 38.462 8.50 5.98 0.00 3.77
307 2060 6.440436 GCGGAATTTTTAAAACACAGGTAGA 58.560 36.000 0.00 0.00 0.00 2.59
311 2064 4.291783 TCGCGGAATTTTTAAAACACAGG 58.708 39.130 6.13 0.00 0.00 4.00
313 2066 6.255887 ACAATTCGCGGAATTTTTAAAACACA 59.744 30.769 6.13 0.00 39.82 3.72
379 2132 2.872858 GGGTCATTCTAGAATTCGGTGC 59.127 50.000 15.49 2.83 0.00 5.01
388 2141 4.227197 GGGATTCTCAGGGTCATTCTAGA 58.773 47.826 0.00 0.00 0.00 2.43
398 2151 1.272092 TGTTTGCTGGGATTCTCAGGG 60.272 52.381 15.28 0.00 33.16 4.45
582 3059 5.939883 TCAATTAGTAAGCTGACACAAGCAT 59.060 36.000 3.43 0.00 46.08 3.79
650 3127 4.372656 AGCGCCTTCAATTAGTAAGCTAG 58.627 43.478 2.29 0.00 0.00 3.42
651 3128 4.402056 AGCGCCTTCAATTAGTAAGCTA 57.598 40.909 2.29 0.00 0.00 3.32
652 3129 3.268023 AGCGCCTTCAATTAGTAAGCT 57.732 42.857 2.29 0.00 0.00 3.74
1005 5423 1.863267 TGGCGATTTTTGCAAAGGTG 58.137 45.000 12.41 5.33 0.00 4.00
1017 5435 0.911769 TGAGGAGTTCCATGGCGATT 59.088 50.000 6.96 0.00 38.89 3.34
1837 6284 2.542907 CGCTGACTGGGTTTGCGTT 61.543 57.895 0.00 0.00 41.45 4.84
1882 6338 1.934589 TTGACATTATCCCGCGTGAG 58.065 50.000 4.92 0.00 0.00 3.51
2020 10134 2.754002 ACTAGTAGAACTCCCTCGCAAC 59.246 50.000 3.59 0.00 0.00 4.17
2060 10634 3.190535 CGGTTCCAAAATACTTGTCCTGG 59.809 47.826 0.00 0.00 0.00 4.45
2215 10837 6.825721 CCTTTTCTTTCAGGCAGTCATATACT 59.174 38.462 0.00 0.00 39.81 2.12
2226 10848 4.590850 ACATGTTCCTTTTCTTTCAGGC 57.409 40.909 0.00 0.00 0.00 4.85
2243 10865 6.402118 CGTCACCACAATAGTAGGAAAACATG 60.402 42.308 0.00 0.00 0.00 3.21
2246 10868 4.992951 ACGTCACCACAATAGTAGGAAAAC 59.007 41.667 0.00 0.00 0.00 2.43
2423 11056 1.203994 TCGAGGTCGGATTCTTCAACC 59.796 52.381 0.00 0.00 40.29 3.77
2675 11308 2.461695 CAGCTTCCCTTGAGGTCTAGA 58.538 52.381 0.00 0.00 36.75 2.43
2946 11581 0.321564 GTCTATGTGGGCACTGCACA 60.322 55.000 0.41 0.41 40.85 4.57
2990 11625 8.573035 ACATTTATAGGTTGTTTGTAGGTGTTG 58.427 33.333 0.00 0.00 0.00 3.33
2991 11626 8.700439 ACATTTATAGGTTGTTTGTAGGTGTT 57.300 30.769 0.00 0.00 0.00 3.32
3038 11673 6.838382 TGCTAAATTTAGGGGGTAGAGAATC 58.162 40.000 23.37 5.74 0.00 2.52
3046 11681 5.012664 CCAAACTTTGCTAAATTTAGGGGGT 59.987 40.000 23.37 0.00 0.00 4.95
3130 11769 0.740868 AGCACCGATGATGGTTCACG 60.741 55.000 0.00 0.00 41.38 4.35
3146 11785 3.519107 TCTCTCTCTCTCTCTCTCAAGCA 59.481 47.826 0.00 0.00 0.00 3.91
3227 12098 9.757227 TCTTTTCCGAATTCAAACATTACAAAT 57.243 25.926 6.22 0.00 0.00 2.32
3329 12203 2.603110 CTCGTATACTTGTGCGCAATGT 59.397 45.455 14.00 14.04 33.65 2.71
3367 12245 5.091261 ACTTGAACTCCTCCATATCACAC 57.909 43.478 0.00 0.00 0.00 3.82
3470 12348 9.379791 AGAGTAAATACAACAACAGGCTTATAC 57.620 33.333 0.00 0.00 0.00 1.47
3481 12359 6.177610 GTGGGGATCAGAGTAAATACAACAA 58.822 40.000 0.00 0.00 0.00 2.83
3504 12382 0.615544 TCCCCGGTCCAAGTAATCGT 60.616 55.000 0.00 0.00 0.00 3.73
3509 12387 2.120940 TGCTCCCCGGTCCAAGTA 59.879 61.111 0.00 0.00 0.00 2.24
3544 12423 1.074405 TCAGTTTCATCTTGGGCAGCT 59.926 47.619 0.00 0.00 0.00 4.24
3545 12424 1.538047 TCAGTTTCATCTTGGGCAGC 58.462 50.000 0.00 0.00 0.00 5.25
3546 12425 2.353889 CGATCAGTTTCATCTTGGGCAG 59.646 50.000 0.00 0.00 0.00 4.85
3556 12435 5.700832 AGTTGTTGCTAATCGATCAGTTTCA 59.299 36.000 0.00 0.00 0.00 2.69
3614 12497 7.033530 ACTAGTACATCTCAGCACTATTCAC 57.966 40.000 0.00 0.00 0.00 3.18
3615 12498 8.926092 ATACTAGTACATCTCAGCACTATTCA 57.074 34.615 4.31 0.00 0.00 2.57
3619 12502 9.794719 ACAATATACTAGTACATCTCAGCACTA 57.205 33.333 4.31 0.00 0.00 2.74
3620 12503 8.572185 CACAATATACTAGTACATCTCAGCACT 58.428 37.037 4.31 0.00 0.00 4.40
3621 12504 7.327275 GCACAATATACTAGTACATCTCAGCAC 59.673 40.741 4.31 0.00 0.00 4.40
3622 12505 7.014230 TGCACAATATACTAGTACATCTCAGCA 59.986 37.037 4.31 7.96 0.00 4.41
3623 12506 7.371159 TGCACAATATACTAGTACATCTCAGC 58.629 38.462 4.31 5.51 0.00 4.26
3624 12507 9.351570 CATGCACAATATACTAGTACATCTCAG 57.648 37.037 4.31 0.00 0.00 3.35
3625 12508 8.860088 ACATGCACAATATACTAGTACATCTCA 58.140 33.333 4.31 0.00 0.00 3.27
3626 12509 9.347934 GACATGCACAATATACTAGTACATCTC 57.652 37.037 4.31 0.00 0.00 2.75
3627 12510 9.083422 AGACATGCACAATATACTAGTACATCT 57.917 33.333 4.31 0.00 0.00 2.90
3636 12519 9.618890 ACAAGAAATAGACATGCACAATATACT 57.381 29.630 0.00 0.00 0.00 2.12
3639 12522 9.394767 TGTACAAGAAATAGACATGCACAATAT 57.605 29.630 0.00 0.00 0.00 1.28
3640 12523 8.785329 TGTACAAGAAATAGACATGCACAATA 57.215 30.769 0.00 0.00 0.00 1.90
3641 12524 7.686438 TGTACAAGAAATAGACATGCACAAT 57.314 32.000 0.00 0.00 0.00 2.71
3642 12525 7.012799 TGTTGTACAAGAAATAGACATGCACAA 59.987 33.333 8.98 0.00 0.00 3.33
3643 12526 6.484977 TGTTGTACAAGAAATAGACATGCACA 59.515 34.615 8.98 0.00 0.00 4.57
3644 12527 6.898041 TGTTGTACAAGAAATAGACATGCAC 58.102 36.000 8.98 0.00 0.00 4.57
3645 12528 7.503521 TTGTTGTACAAGAAATAGACATGCA 57.496 32.000 15.21 0.00 32.34 3.96
3646 12529 8.970691 AATTGTTGTACAAGAAATAGACATGC 57.029 30.769 20.56 0.20 41.94 4.06
3649 12532 8.289618 GCAGAATTGTTGTACAAGAAATAGACA 58.710 33.333 20.56 5.52 41.94 3.41
3650 12533 8.507249 AGCAGAATTGTTGTACAAGAAATAGAC 58.493 33.333 20.56 11.31 41.94 2.59
3651 12534 8.621532 AGCAGAATTGTTGTACAAGAAATAGA 57.378 30.769 20.56 0.00 41.94 1.98
3655 12538 9.862371 TTTTTAGCAGAATTGTTGTACAAGAAA 57.138 25.926 20.56 13.07 41.94 2.52
3656 12539 9.296400 GTTTTTAGCAGAATTGTTGTACAAGAA 57.704 29.630 19.22 19.22 41.94 2.52
3657 12540 8.682710 AGTTTTTAGCAGAATTGTTGTACAAGA 58.317 29.630 8.98 4.62 41.94 3.02
3658 12541 8.856490 AGTTTTTAGCAGAATTGTTGTACAAG 57.144 30.769 8.98 0.00 41.94 3.16
3662 12545 9.820229 CGATTAGTTTTTAGCAGAATTGTTGTA 57.180 29.630 0.00 0.00 0.00 2.41
3663 12546 7.326063 GCGATTAGTTTTTAGCAGAATTGTTGT 59.674 33.333 0.00 0.00 0.00 3.32
3664 12547 7.538678 AGCGATTAGTTTTTAGCAGAATTGTTG 59.461 33.333 0.00 0.00 0.00 3.33
3665 12548 7.593825 AGCGATTAGTTTTTAGCAGAATTGTT 58.406 30.769 0.00 0.00 0.00 2.83
3666 12549 7.145932 AGCGATTAGTTTTTAGCAGAATTGT 57.854 32.000 0.00 0.00 0.00 2.71
3667 12550 7.852945 CCTAGCGATTAGTTTTTAGCAGAATTG 59.147 37.037 0.00 0.00 0.00 2.32
3668 12551 7.012421 CCCTAGCGATTAGTTTTTAGCAGAATT 59.988 37.037 0.00 0.00 0.00 2.17
3669 12552 6.483640 CCCTAGCGATTAGTTTTTAGCAGAAT 59.516 38.462 0.00 0.00 0.00 2.40
3670 12553 5.815740 CCCTAGCGATTAGTTTTTAGCAGAA 59.184 40.000 0.00 0.00 0.00 3.02
3671 12554 5.128171 TCCCTAGCGATTAGTTTTTAGCAGA 59.872 40.000 0.00 0.00 0.00 4.26
3672 12555 5.357257 TCCCTAGCGATTAGTTTTTAGCAG 58.643 41.667 0.00 0.00 0.00 4.24
3673 12556 5.347620 TCCCTAGCGATTAGTTTTTAGCA 57.652 39.130 0.00 0.00 0.00 3.49
3674 12557 6.089150 CGTATCCCTAGCGATTAGTTTTTAGC 59.911 42.308 0.00 0.00 0.00 3.09
3675 12558 6.089150 GCGTATCCCTAGCGATTAGTTTTTAG 59.911 42.308 0.00 0.00 0.00 1.85
3676 12559 5.922544 GCGTATCCCTAGCGATTAGTTTTTA 59.077 40.000 0.00 0.00 0.00 1.52
3677 12560 4.748600 GCGTATCCCTAGCGATTAGTTTTT 59.251 41.667 0.00 0.00 0.00 1.94
3678 12561 4.304939 GCGTATCCCTAGCGATTAGTTTT 58.695 43.478 0.00 0.00 0.00 2.43
3679 12562 3.910648 GCGTATCCCTAGCGATTAGTTT 58.089 45.455 0.00 0.00 0.00 2.66
3680 12563 3.572604 GCGTATCCCTAGCGATTAGTT 57.427 47.619 0.00 0.00 0.00 2.24
3688 12571 3.284133 GAGGCCGCGTATCCCTAGC 62.284 68.421 4.92 0.00 0.00 3.42
3689 12572 2.637383 GGAGGCCGCGTATCCCTAG 61.637 68.421 4.92 0.00 0.00 3.02
3690 12573 2.599578 GGAGGCCGCGTATCCCTA 60.600 66.667 4.92 0.00 0.00 3.53
3709 12592 4.821589 GGGTTCTCTCCCGCTGCG 62.822 72.222 16.34 16.34 37.93 5.18
3715 12598 4.097361 GCGGTGGGGTTCTCTCCC 62.097 72.222 0.00 0.00 46.31 4.30
3716 12599 4.097361 GGCGGTGGGGTTCTCTCC 62.097 72.222 0.00 0.00 0.00 3.71
3717 12600 4.452733 CGGCGGTGGGGTTCTCTC 62.453 72.222 0.00 0.00 0.00 3.20
3735 12618 4.598894 CAGGAGATCAGGCGGCGG 62.599 72.222 9.78 1.99 0.00 6.13
3737 12620 4.925861 GGCAGGAGATCAGGCGGC 62.926 72.222 0.00 0.00 0.00 6.53
3738 12621 3.160047 AGGCAGGAGATCAGGCGG 61.160 66.667 0.00 0.00 0.00 6.13
3739 12622 2.420890 GAGGCAGGAGATCAGGCG 59.579 66.667 0.00 0.00 0.00 5.52
3740 12623 2.828145 GGAGGCAGGAGATCAGGC 59.172 66.667 0.00 0.00 0.00 4.85
3741 12624 2.506061 CCGGAGGCAGGAGATCAGG 61.506 68.421 0.00 0.00 46.14 3.86
3742 12625 3.136750 CCGGAGGCAGGAGATCAG 58.863 66.667 0.00 0.00 46.14 2.90
3754 12637 3.003173 TGAAGGAGGTGGCCGGAG 61.003 66.667 5.05 0.00 0.00 4.63
3755 12638 3.319198 GTGAAGGAGGTGGCCGGA 61.319 66.667 5.05 0.00 0.00 5.14
3756 12639 3.190738 TTGTGAAGGAGGTGGCCGG 62.191 63.158 0.00 0.00 0.00 6.13
3757 12640 1.966451 GTTGTGAAGGAGGTGGCCG 60.966 63.158 0.00 0.00 0.00 6.13
3758 12641 0.890996 CTGTTGTGAAGGAGGTGGCC 60.891 60.000 0.00 0.00 0.00 5.36
3759 12642 0.108585 TCTGTTGTGAAGGAGGTGGC 59.891 55.000 0.00 0.00 0.00 5.01
3760 12643 1.694150 TCTCTGTTGTGAAGGAGGTGG 59.306 52.381 0.00 0.00 0.00 4.61
3761 12644 2.366916 AGTCTCTGTTGTGAAGGAGGTG 59.633 50.000 0.00 0.00 0.00 4.00
3762 12645 2.683768 AGTCTCTGTTGTGAAGGAGGT 58.316 47.619 0.00 0.00 0.00 3.85
3763 12646 4.082845 TCTAGTCTCTGTTGTGAAGGAGG 58.917 47.826 0.00 0.00 0.00 4.30
3764 12647 5.652014 AGATCTAGTCTCTGTTGTGAAGGAG 59.348 44.000 0.00 0.00 28.45 3.69
3765 12648 5.417266 CAGATCTAGTCTCTGTTGTGAAGGA 59.583 44.000 13.60 0.00 36.26 3.36
3766 12649 5.417266 TCAGATCTAGTCTCTGTTGTGAAGG 59.583 44.000 18.33 0.00 40.79 3.46
3767 12650 6.507958 TCAGATCTAGTCTCTGTTGTGAAG 57.492 41.667 18.33 0.00 40.79 3.02
3768 12651 6.901081 TTCAGATCTAGTCTCTGTTGTGAA 57.099 37.500 18.33 8.01 40.79 3.18
3769 12652 6.294787 GGTTTCAGATCTAGTCTCTGTTGTGA 60.295 42.308 18.33 3.74 40.79 3.58
3770 12653 5.866633 GGTTTCAGATCTAGTCTCTGTTGTG 59.133 44.000 18.33 1.98 40.79 3.33
3771 12654 5.046950 GGGTTTCAGATCTAGTCTCTGTTGT 60.047 44.000 18.33 0.00 40.79 3.32
3772 12655 5.186797 AGGGTTTCAGATCTAGTCTCTGTTG 59.813 44.000 18.33 2.51 40.79 3.33
3773 12656 5.337788 AGGGTTTCAGATCTAGTCTCTGTT 58.662 41.667 18.33 3.85 40.79 3.16
3774 12657 4.941713 AGGGTTTCAGATCTAGTCTCTGT 58.058 43.478 18.33 3.03 40.79 3.41
3775 12658 5.200483 AGAGGGTTTCAGATCTAGTCTCTG 58.800 45.833 14.94 14.94 41.23 3.35
3776 12659 5.193728 AGAGAGGGTTTCAGATCTAGTCTCT 59.806 44.000 0.00 2.69 34.00 3.10
3777 12660 5.445964 AGAGAGGGTTTCAGATCTAGTCTC 58.554 45.833 0.00 0.06 34.00 3.36
3778 12661 5.466127 AGAGAGGGTTTCAGATCTAGTCT 57.534 43.478 0.00 0.00 37.80 3.24
3779 12662 5.654650 TGAAGAGAGGGTTTCAGATCTAGTC 59.345 44.000 0.00 0.00 0.00 2.59
3780 12663 5.584913 TGAAGAGAGGGTTTCAGATCTAGT 58.415 41.667 0.00 0.00 0.00 2.57
3781 12664 6.239289 GGATGAAGAGAGGGTTTCAGATCTAG 60.239 46.154 0.00 0.00 36.81 2.43
3782 12665 5.600484 GGATGAAGAGAGGGTTTCAGATCTA 59.400 44.000 0.00 0.00 36.81 1.98
3783 12666 4.408596 GGATGAAGAGAGGGTTTCAGATCT 59.591 45.833 0.00 0.00 36.81 2.75
3784 12667 4.163078 TGGATGAAGAGAGGGTTTCAGATC 59.837 45.833 0.00 0.00 36.81 2.75
3785 12668 4.107072 TGGATGAAGAGAGGGTTTCAGAT 58.893 43.478 0.00 0.00 36.81 2.90
3786 12669 3.520696 TGGATGAAGAGAGGGTTTCAGA 58.479 45.455 0.00 0.00 36.81 3.27
3787 12670 3.988976 TGGATGAAGAGAGGGTTTCAG 57.011 47.619 0.00 0.00 36.81 3.02
3788 12671 3.200825 GGATGGATGAAGAGAGGGTTTCA 59.799 47.826 0.00 0.00 37.68 2.69
3789 12672 3.434310 GGGATGGATGAAGAGAGGGTTTC 60.434 52.174 0.00 0.00 0.00 2.78
3790 12673 2.511637 GGGATGGATGAAGAGAGGGTTT 59.488 50.000 0.00 0.00 0.00 3.27
3791 12674 2.131023 GGGATGGATGAAGAGAGGGTT 58.869 52.381 0.00 0.00 0.00 4.11
3792 12675 1.813102 GGGATGGATGAAGAGAGGGT 58.187 55.000 0.00 0.00 0.00 4.34
3793 12676 0.683973 CGGGATGGATGAAGAGAGGG 59.316 60.000 0.00 0.00 0.00 4.30
3794 12677 0.683973 CCGGGATGGATGAAGAGAGG 59.316 60.000 0.00 0.00 42.00 3.69
3795 12678 1.709578 TCCGGGATGGATGAAGAGAG 58.290 55.000 0.00 0.00 43.74 3.20
3796 12679 3.946242 TCCGGGATGGATGAAGAGA 57.054 52.632 0.00 0.00 43.74 3.10
3805 12688 4.227134 CGCTGGACTCCGGGATGG 62.227 72.222 0.00 0.00 40.09 3.51
3806 12689 2.427540 GATCGCTGGACTCCGGGATG 62.428 65.000 17.91 0.00 33.15 3.51
3807 12690 2.123251 ATCGCTGGACTCCGGGAT 60.123 61.111 0.00 9.21 0.00 3.85
3808 12691 2.833582 GATCGCTGGACTCCGGGA 60.834 66.667 0.00 7.44 0.00 5.14
3809 12692 3.917760 GGATCGCTGGACTCCGGG 61.918 72.222 0.00 0.00 0.00 5.73
3810 12693 2.835431 AGGATCGCTGGACTCCGG 60.835 66.667 0.00 0.00 34.13 5.14
3811 12694 2.415010 CAGGATCGCTGGACTCCG 59.585 66.667 3.90 0.00 34.13 4.63
3812 12695 2.801631 CCCAGGATCGCTGGACTCC 61.802 68.421 24.11 0.00 44.39 3.85
3813 12696 2.818132 CCCAGGATCGCTGGACTC 59.182 66.667 24.11 0.00 44.39 3.36
3814 12697 3.474570 GCCCAGGATCGCTGGACT 61.475 66.667 24.11 0.00 44.39 3.85
3815 12698 4.899239 CGCCCAGGATCGCTGGAC 62.899 72.222 24.11 15.70 44.39 4.02
3817 12700 4.899239 GTCGCCCAGGATCGCTGG 62.899 72.222 18.45 18.45 41.45 4.85
3818 12701 3.781770 GAGTCGCCCAGGATCGCTG 62.782 68.421 4.67 4.67 0.00 5.18
3819 12702 3.532155 GAGTCGCCCAGGATCGCT 61.532 66.667 0.00 0.00 0.00 4.93
3820 12703 4.933064 CGAGTCGCCCAGGATCGC 62.933 72.222 0.00 0.00 0.00 4.58
3821 12704 3.187699 CTCGAGTCGCCCAGGATCG 62.188 68.421 7.92 0.00 34.80 3.69
3822 12705 2.725008 CTCGAGTCGCCCAGGATC 59.275 66.667 7.92 0.00 0.00 3.36
3823 12706 2.835431 CCTCGAGTCGCCCAGGAT 60.835 66.667 12.31 0.00 0.00 3.24
3862 12745 1.064389 AGGAAAAGGAGGTGGCTATGC 60.064 52.381 0.00 0.00 0.00 3.14
3863 12746 2.422093 GGAGGAAAAGGAGGTGGCTATG 60.422 54.545 0.00 0.00 0.00 2.23
3864 12747 1.847088 GGAGGAAAAGGAGGTGGCTAT 59.153 52.381 0.00 0.00 0.00 2.97
3865 12748 1.286248 GGAGGAAAAGGAGGTGGCTA 58.714 55.000 0.00 0.00 0.00 3.93
3866 12749 1.501654 GGGAGGAAAAGGAGGTGGCT 61.502 60.000 0.00 0.00 0.00 4.75
3867 12750 1.000771 GGGAGGAAAAGGAGGTGGC 60.001 63.158 0.00 0.00 0.00 5.01
3868 12751 1.004862 GAAGGGAGGAAAAGGAGGTGG 59.995 57.143 0.00 0.00 0.00 4.61
3869 12752 1.004862 GGAAGGGAGGAAAAGGAGGTG 59.995 57.143 0.00 0.00 0.00 4.00
3870 12753 1.132036 AGGAAGGGAGGAAAAGGAGGT 60.132 52.381 0.00 0.00 0.00 3.85
3871 12754 1.562008 GAGGAAGGGAGGAAAAGGAGG 59.438 57.143 0.00 0.00 0.00 4.30
3872 12755 1.208293 CGAGGAAGGGAGGAAAAGGAG 59.792 57.143 0.00 0.00 0.00 3.69
3873 12756 1.276622 CGAGGAAGGGAGGAAAAGGA 58.723 55.000 0.00 0.00 0.00 3.36
3874 12757 0.393132 GCGAGGAAGGGAGGAAAAGG 60.393 60.000 0.00 0.00 0.00 3.11
3875 12758 0.393132 GGCGAGGAAGGGAGGAAAAG 60.393 60.000 0.00 0.00 0.00 2.27
3876 12759 1.683441 GGCGAGGAAGGGAGGAAAA 59.317 57.895 0.00 0.00 0.00 2.29
3877 12760 2.656069 CGGCGAGGAAGGGAGGAAA 61.656 63.158 0.00 0.00 0.00 3.13
3878 12761 3.075005 CGGCGAGGAAGGGAGGAA 61.075 66.667 0.00 0.00 0.00 3.36


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.